COMPUTO

A new born academic journal promoting reproducibility
Supported by the French Statistical Society

Last update: June 2022

Editorial Board

Chloé-Agathe Azencott

Machine Learning for therapeutic research
Mines ParisTech, Inserm, Institut Curie

Pierre Neuvial

Statistics,
CNRS, Institut de Mathématiques de Toulouse

Julien Chiquet (Chief Editor)

Statistical learning for life science
Université Paris-Saclay, AgroParisTech, INRAE

Nelle Varoquaux

Machine learning and causal inference for genomics
CNRS, Université Grenoble Alpes

Facts in Stats/ML academic publications

Multiplication of academic journals and articles
→ at the expense of quality / scientific accuracy?
Lack of valorisation of computer/algorithmic developments and case studies
Saturation of existing solutions
Rapid evolution of tools
- Great API (Rstudio, VScode)
- Scientific Publishing system (quarto, Jupyter)
- Integration / dynamics (git(hub), Actions)

Computo’s Board Positioning

Need to renew the mode of publication of scientific knowledge and know-how

Existing solutions

Standard academic journals

Statistics and Computing, Computational Statistics and Data Analysis, Journal of Computational and Graphical Statistics, JMLR, JRSS-B, JASA, …

Limitations

Fixed format (non-dynamic typically, PDF) limiting reproducibility

Software journals

R journal, Journal of Statistical Software, Journal of Open Source Software, JMLR Machine Learning Open Source Software, ROpen-Sci…

Limitations

Congestion, language-centric, software documentation, not structured around a scientific question

Computo in a nutshell

Aims and Scope

Promote contributions in statistics and machine learning that provide insight into which models/methods are the most appropriate to a specific question.

Open and reproducible

reproducibility of numerical results is a necessary condition for publication
all necessary data and code must be available.
reviews are open (reviewers can remain anonymous)

Assessing reproducibility

At the submission stage!

How does Computo work? (1/3)

How does Computo work? (2/3)

1. Advanced notebook System

https://quarto.org (embed Jupyter and RMarkdown)

Code (Python/Julia/R)
Math (\(\LaTeX\))
Biblio (\(bibTeX\))
Interactivity (HTML widget, CSS)

2. Git repository and services

github/github-action

Continuous Integration (reproducibility script)
Projects Management (submission, publication)
Issues (reviewing, discussion)

How does Computo work? (3/3)

3. Container service

binder

Easy to customize
Easy to interface with github

4. Reviewing system

Scholastica

Discussion among Editorial board
Reviewer Invitation
Anonymous exchanges between authors/reviewers

→ Eventually published (as Issues)

Author point of view (1/4)

Step 0: setup a github repository

Copy our template repository to use it as a starter

Author point of view (2/4)

Step 1. write your contribution

Write your notebook as usual (Same spirit as Jupyter/Rmarkdown).

Step 2: configure your conda/binder environment

file environment.yml

name: computorbuild
channels:
  - conda-forge
dependencies:
  - jupyter
  - numpy
  - r-base=4.2.0

Author point of view (3/4)

Step 3: proof reproducibility

A git push will trigger build process on github

name: build
on: push
jobs:
  computorticle:
    runs-on: ubuntu-latest
    steps: # [...]
      - name: Installing dependencies with Miniconda
        uses: conda-incubator/setup-miniconda@v2
          environment-file: environment.yml
        # [...]
      - name: Rendering with Quarto
        run: quarto render content.qmd
        # [...]
      - name: Deploying article on github pages
        # [...]

Author point of view (4/4)

Step 4. submit

If the build process is successful,

An HTML version is pushed on a github-page
A PDF version can be obtained via chrome-print
a binder repos can be associated

→ Submit the PDF on Scholastica page

See our quarto template for more

Editor point of view

Once the reviewing process has ended (successfully!)

Copy the author’s repository
Format to the final version
Publish reviews as issues
Add entry on the Journal web site referring
- github repository
- data repository
- reviewing

See our mock contribution for more

First published paper

https://github.com/computorg/published-202204-deeplearning-occupancy-lynx

Computo’s first year review

framework functional + doi, ISSN, etc.
1 published article, 3 articles under review, 2 or 3 promises of submissions
3 talks in reproducibilty workshops (Toronto, Humastica, Journée libre accès)
difficulty to find reviewers
neither technical nor human support

About the Logo

How could you help?

Authoring

Submit your work!

Reviewing

Volunteer by filling this form: https://forms.gle/P9iYJANuNM4WTVHDA

Feeding-in Computo with Peer-community-in

Get involved in a stat/ML PCI to feed Computo

Existing skeleton: CompStat PCI https://compstat.peercommunityin.org/
Identified scientific leader: Christian Robert
Technical/Web support needed
Active community of recommenders needed